de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states
Interface DifferentiableState
- All Superinterfaces:
- State
- All Known Implementing Classes:
- SimpleDifferentiableState
public interface DifferentiableState
- extends State
This interface declares a method that allows to evaluate the gradient which is essential for numerical optimization.
- Author:
- Jens Keilwagen
getLogScoreAndPartialDerivation
double getLogScoreAndPartialDerivation(int startPos,
int endPos,
IntList indices,
DoubleList partDer,
Sequence seq)
throws OperationNotSupportedException,
WrongLengthException
- This method allows to compute the logarithm of the score and the gradient for the given subsequences.
- Parameters:
startPos
- the start position (inclusive)endPos
- the end position (inclusive)indices
- a list for the parameter indicespartDer
- a list for the partial derivationsseq
- the Sequence
(s)
- Returns:
- the logarithm of the score
- Throws:
WrongLengthException
- if the length can not be modeled
OperationNotSupportedException
- if the reverse complement of the sequence can not be computed